Mercurial > repos > iuc > straindesign_analyzing_model

annotate analyzing-model.xml @ 1:3b09226992ff draft default tip

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planemo upload for repository https://github.com/brsynth/straindesign commit 64ebfca7e5fd855b5d887974e39040c125193626
author iuc
date Mon, 20 Feb 2023 10:01:24 +0000
parents 490a37e24bed
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490a37e24bed planemo upload for repository https://github.com/brsynth/straindesign commit 593e182e67109bd8649ddec5bf5b97d1a4531b3f
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1 <tool id="straindesign_analyzing_model" name="StrainDesign analyzing-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
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2 <description>Produce a pareto plot for a biological model</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## Run cmdline
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10 python -m straindesign analyzing-model
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11 @CMD_INPUT_MODEL@
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12 @CMD_INPUT_MEDIUM@
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13 @CMD_BIOMASS_RXN_ID@
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14 @CMD_TARGET_RXN_ID@
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15 @CMD_INPUT_PATHWAY@
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16 #if str('$substrate_cond.substrate_param') == 'yes'
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17 --substrate-rxn-id '$substrate_cond.substrate_rxn_id'
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18 #end if
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19 --output-pareto-png '$output_png'
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20 ]]></command>
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21 <expand macro="env_variables"/>
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22 <inputs>
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23 <expand macro="input_model_sbml"/>
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24 <expand macro="input_medium_tsv"/>
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25 <expand macro="input_biomass_rxn_id"/>
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26 <expand macro="input_target_rxn_id"/>
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27 <expand macro="input_pathway_sbml"/>
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28 <conditional name="substrate_cond">
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29 <param name="substrate_param" type="select" label="Provide a substrate reaction" help="Choose yourself a carbon source or it will be detected automatically">
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30 <option value="yes">yes</option>
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31 <option value="no" selected="true">No</option>
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32 </param>
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33 <when value="yes">
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34 <expand macro="input_substrate_rxn_id"/>
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35 </when>
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36 <when value="no"/>
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37 </conditional>
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38 </inputs>
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39 <outputs>
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40 <data name="output_png" format="png" label="${tool.name}" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <!-- test 1 -->
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45 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
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46 <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
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47 <param name="target_rxn_id" value="EX_tyrp_e" />
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48 <output name="output_png" ftype="png">
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49 <assert_contents>
1
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50 <has_size value="30000" delta="10000"/>
0
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51 </assert_contents>
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52 </output>
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53 </test>
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54 <test>
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55 <!-- test 2 -->
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56 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
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57 <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
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58 <param name="target_rxn_id" value="EX_tyrp_e" />
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59 <param name="substrate_rxn_id" value="EX_glc__D_e" />
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60 <output name="output_png" ftype="png">
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61 <assert_contents>
1
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62 <has_size value="30000" delta="10000"/>
0
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63 </assert_contents>
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64 </output>
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65 </test>
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66 <test>
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67 <!-- test 3 -->
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68 <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
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69 <param name="pathway" ftype="sbml" value="butanol.xml" />
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70 <param name="medium" ftype="tabular" value="butanol.tsv" />
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71 <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
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72 <param name="substrate_rxn_id" value="EX_glc__D_e" />
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73 <param name="target_rxn_id" value="EX_1btol_e" />
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74 <output name="output_png" ftype="png">
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75 <assert_contents>
1
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76 <has_size value="30000" delta="10000"/>
0
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77 </assert_contents>
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78 </output>
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82 @HELP_TITLE@
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83
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84 This tool produces a phenotypic-phase-plane plot given these datas:
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85 * model
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86 * reaction producing a target
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87 * biomass reaction
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88 These informations are optionals and will be adapted to your needs:
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89 * an heterologous pathway
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90 * a carbon substrate
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91 * media composition
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92
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93 @HELP_LINK@
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94 ]]></help>
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95 <expand macro="creator"/>
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96 <expand macro="citation"/>
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97 </tool>